Package org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency

Enum Class FrequencySource

java.lang.Object
java.lang.Enum<FrequencySource>
org.monarchinitiative.lirical.exomiser_db_adapter.model.frequency.FrequencySource
All Implemented Interfaces:
Serializable, Comparable<FrequencySource>, Constable
public enum FrequencySource extends Enum<FrequencySource>
Enum describing where the frequency data has originated.
Author:
Damian Smedley <damian.smedley@sanger.ac.uk>, Jules Jacobsen <jules.jacobsen@sanger.ac.uk>

  • Enum Constant Details

  • Field Details

    • ALL_ESP_SOURCES

      public static final Set<FrequencySource> ALL_ESP_SOURCES

    • ALL_EXAC_SOURCES

      public static final Set<FrequencySource> ALL_EXAC_SOURCES

    • ALL_GNOMAD_SOURCES

      public static final Set<FrequencySource> ALL_GNOMAD_SOURCES

    • ALL_ALFA_SOURCES

      public static final Set<FrequencySource> ALL_ALFA_SOURCES

    • ALL_EXTERNAL_FREQ_SOURCES

      public static final Set<FrequencySource> ALL_EXTERNAL_FREQ_SOURCES

    • NON_FOUNDER_POPS

      public static final Set<FrequencySource> NON_FOUNDER_POPS
      Returns the set of non-founder/bottle-necked populations for use in frequency filtering. Here we're using the populations included in the gnomAD filtering allele frequency. Note that this is related to the ClinGen recommendations for populations to consider for filtering against when considering the BA1 (Benign standAlone) evidence category. More explicitly, this means any FrequencySource excluding Ashkenazi Jewish (ASJ), European Finnish (FIN), and "Other" (OTH) populations (gnomAD v2) or Amish (AMI), Ashkenazi Jewish (ASJ), European Finnish (FIN), Middle Eastern (MID), and "Other" (OTH) populations (gnomAD v3).
      Since:
      13.3.0

  • Method Details

    • values

      public static FrequencySource[] values()
      Returns an array containing the constants of this enum class, in the order they are declared.
      Returns:
      an array containing the constants of this enum class, in the order they are declared

    • valueOf

      public static FrequencySource valueOf(String name)
      Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)
      Parameters:
      name - the name of the enum constant to be returned.
      Returns:
      the enum constant with the specified name
      Throws:
      IllegalArgumentException - if this enum class has no constant with the specified name
      NullPointerException - if the argument is null

    • getSource

      public String getSource()

    • isGnomadSource

      public boolean isGnomadSource()